CAVE: Connectome Annotation Versioning Engine DOI Creative Commons
Sven Dorkenwald, Casey M Schneider-Mizell, Derrick Brittain

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: July 28, 2023

Abstract Advances in Electron Microscopy, image segmentation and computational infrastructure have given rise to large-scale richly annotated connectomic datasets which are increasingly shared across communities. To enable collaboration, users need be able concurrently create new annotations correct errors the automated by proofreading. In large datasets, every proofreading edit relabels cell identities of millions voxels thousands like synapses. For analysis, require immediate reproducible access this constantly changing expanding data landscape. Here, we present Connectome Annotation Versioning Engine (CAVE), a for connectome analysis up-to petascale (∼1mm 3 ) while annotating is ongoing. segmentation, CAVE provides distributed continuous versioning reconstructions. Annotations defined locations such that they can quickly assigned underlying segment enables fast queries CAVE’s arbitrary time points. supports schematized, extensible annotations, so researchers readily design novel annotation types. already used many connectomics including largest available date.

Language: Английский

A connectome and analysis of the adult Drosophila central brain DOI Creative Commons
Louis K. Scheffer, C. Shan Xu, Michał Januszewski

et al.

eLife, Journal Year: 2020, Volume and Issue: 9

Published: Sept. 3, 2020

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction brain fruit fly Drosophila melanogaster . Improved include procedures to prepare, image, align, segment, find synapses in, proofread such data sets. define cell types, refine computational compartments, provide an exhaustive atlas examples many them novel. detailed consisting neurons their chemical most central brain. make public simplify access, reducing effort needed answer circuit questions, linking defined by our analysis with genetic reagents. Biologically, we examine distributions connection strengths, motifs on different scales, electrical consequences compartmentalization, evidence that maximizing packing density is important criterion in evolution fly’s

Language: Английский

Citations

996
FlyWire: online community for whole-brain connectomics DOI
Sven Dorkenwald, Claire McKellar, Thomas Macrina

et al.

Nature Methods, Journal Year: 2021, Volume and Issue: 19(1), P. 119 - 128

Published: Dec. 23, 2021

Language: Английский

Citations

228
Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity DOI Creative Commons
Nicholas L. Turner, Thomas Macrina, J. Alexander Bae

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(6), P. 1082 - 1100.e24

Published: Feb. 24, 2022

Language: Английский

Citations

155
Neuronal wiring diagram of an adult brain DOI Creative Commons
Sven Dorkenwald, Arie Matsliah, Amy Sterling

et al.

Nature, Journal Year: 2024, Volume and Issue: 634(8032), P. 124 - 138

Published: Oct. 2, 2024

Language: Английский

Citations

147
Neuronal wiring diagram of an adult brain DOI Creative Commons
Sven Dorkenwald, Arie Matsliah, Amy Sterling

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 30, 2023

Abstract Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains reconstruct local connectivity maps that are highly informative, yet inadequate for understanding function more globally. Here, we present the first neuronal wiring diagram a whole adult brain, containing 5×10 7 chemical synapses ∼130,000 reconstructed from female Drosophila melanogaster . The resource also incorporates annotations cell classes types, nerves, hemilineages, predictions neurotransmitter identities. Data products available download, programmatic access, interactive browsing made interoperable with other fly data resources. We show how derive projectome, map projections regions, connectome. demonstrate tracing synaptic pathways analysis information flow inputs (sensory ascending neurons) outputs (motor, endocrine, descending neurons), across both hemispheres, central optic lobes. Tracing subset photoreceptors all way motor illustrates structure uncover putative circuit mechanisms underlying sensorimotor behaviors. technologies open ecosystem FlyWire Consortium set stage future large-scale connectome projects in species.

Language: Английский

Citations

135
Oligodendrocyte precursor cells ingest axons in the mouse neocortex DOI Creative Commons
JoAnn Buchanan, Leila Elabbady, Forrest Collman

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(48)

Published: Nov. 23, 2022

Neurons in the developing brain undergo extensive structural refinement as nascent circuits adopt their mature form. This physical transformation of neurons is facilitated by engulfment and degradation axonal branches synapses surrounding glial cells, including microglia astrocytes. However, small size phagocytic organelles complex, highly ramified morphology glia have made it difficult to define contribution these other cell types this crucial process. Here, we used large-scale, serial section transmission electron microscopy (TEM) with computational volume segmentation reconstruct complete 3D morphologies distinct mouse visual cortex, providing unprecedented resolution composition. Unexpectedly, discovered that fine processes oligodendrocyte precursor cells (OPCs), a population abundant, dynamic progenitors, frequently surrounded axons. Numerous phagosomes phagolysosomes (PLs) containing fragments axons vesicular structures were present inside processes, suggesting OPCs engage axon pruning. Single-nucleus RNA sequencing from cortex revealed express key genes at stage, well neuronal transcripts, consistent active engulfment. Although are thought be responsible for majority synaptic pruning refinement, PLs ten times more abundant than markedly less newly generated oligodendrocytes, contribute substantially during cortical development.

Language: Английский

Citations

105
Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex DOI Creative Commons
Casey M Schneider-Mizell, Ágnes L. Bodor, Derrick Brittain

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 24, 2023

Mammalian cortex features a vast diversity of neuronal cell types, each with characteristic anatomical, molecular and functional properties. Synaptic connectivity powerfully shapes how type participates in the cortical circuit, but mapping rules at resolution distinct types remains difficult. Here, we used millimeter-scale volumetric electron microscopy 1 to investigate all inhibitory neurons across densely-segmented population 1352 cells spanning layers mouse visual cortex, producing wiring diagram connections more than 70,000 synapses. Taking data-driven approach inspired by classical neuroanatomy, classified based on relative targeting dendritic compartments other developed novel classification excitatory morphological synaptic input The between revealed class disinhibitory specialist basket cells, addition familiar subclasses. Analysis onto found widespread specificity, many interneurons exhibiting differential certain subpopulations spatially intermingled potential targets. Inhibitory was organized into “motif groups,” diverse sets that collectively target both perisomatic same Collectively, our analysis identified new organizing principles for inhibition will serve as foundation linking modern multimodal atlases diagram.

Language: Английский

Citations

60
Synaptic wiring motifs in posterior parietal cortex support decision-making DOI
Aaron T. Kuan, Giulio Bondanelli, Laura N. Driscoll

et al.

Nature, Journal Year: 2024, Volume and Issue: 627(8003), P. 367 - 373

Published: Feb. 21, 2024

Language: Английский

Citations

31
Heavy-tailed neuronal connectivity arises from Hebbian self-organization DOI
Christopher W. Lynn, Caroline M. Holmes, Stephanie E. Palmer

et al.

Nature Physics, Journal Year: 2024, Volume and Issue: 20(3), P. 484 - 491

Published: Jan. 17, 2024

Language: Английский

Citations

22
RoboEM: automated 3D flight tracing for synaptic-resolution connectomics DOI Creative Commons
Martin Schmidt, Alessandro Motta, Meike Sievers

et al.

Nature Methods, Journal Year: 2024, Volume and Issue: 21(5), P. 908 - 913

Published: March 21, 2024

Mapping neuronal networks from three-dimensional electron microscopy (3D-EM) data still poses substantial reconstruction challenges, in particular for thin axons. Currently available automated image segmentation methods require manual proofreading many types of connectomic analysis. Here we introduce RoboEM, an artificial intelligence-based self-steering 3D 'flight' system trained to navigate along neurites using only 3D-EM as input. Applied mouse and human cortex, RoboEM substantially improves state-of-the-art segmentations can replace more complex analysis problems, yielding computational annotation cost cortical connectomes about 400-fold lower than the error correction.

Language: Английский

Citations

18